Those 550 fans are pretty solid if the jetting is correct and the carbs are kept clean. The only problem I have ever read about is lean burndowns, the engine itself is very good overall.
I would just do a compression test and if it's good, I would keep running them. I had almost 9000 miles on my last Polaris triple and the rings, pistons, bearings, etc had never been touched. Had it checked out by dealer at 8K miles and they said keep running it, so I did.
If compression is low, and you have kept up with the fogging each year, which helps guard against rusty bearings, I would just do a top-end rebuild now and plan on a total rebuild at 9-10K miles.
Good luck -